NM_014795.3(ZEB2):c.489C>T (p.Ile163=) AND not specified

This record was updated by the submitter. Please see the current version.

Germline classification:: Conflicting classifications of pathogenicity (4 submissions)
Last evaluated:: Apr 10, 2014
Review status:: criteria provided, conflicting classifications

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000081671.8

Allele description

NM_014795.3(ZEB2):c.489C>T (p.Ile163=)

Gene:

ZEB2:zinc finger E-box binding homeobox 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q22.3

Genomic location:

Preferred name:

NM_014795.3(ZEB2):c.489C>T (p.Ile163=)

Other names:

p.I163I:ATC>ATT

HGVS:

NC_000002.12:g.144404939G>A
NG_016431.1:g.120453C>T
NM_014795.3:c.489C>T
NP_055610.1:p.Ile163=
NC_000002.11:g.145162506G>A
NM_014795.2:c.489C>T
NP_055610.1:p.(=)

Links:

dbSNP: rs138859323

GMAF:

0.0016(A), 138859323

NCBI 1000 Genomes Browser:

rs138859323

Allele Frequency:

0.0028, GO-ESP

Molecular consequence:

NM_014795.3:c.489C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

Recent activity

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NT-3 growth factor receptor isoform d precursor [Homo sapiens]
NT-3 growth factor receptor isoform d precursor [Homo sapiens]
gi|340745353|ref|NP_001230030.1|

Protein
Sulku_1283 [Sulfuricurvum kujiense DSM 16994]
Sulku_1283 [Sulfuricurvum kujiense DSM 16994]
Gene ID:10018450

Gene
F52D1.2 Gag-pol polyprotein [Caenorhabditis elegans]
F52D1.2 Gag-pol polyprotein [Caenorhabditis elegans]
Gene ID:186101

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000113602	EGL Genetic Diagnostics,Eurofins Clinical Diagnostics	criteria provided, single submitter (EGL Classification Definitions)	Benign (Sep 13, 2013)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link,
SCV000169860	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Benign (Mar 9, 2012)	germline	clinical testing	Citation Link,
SCV000195500	Genetic Services Laboratory, University of Chicago	criteria provided, single submitter (ACMG Guidelines, 2007)	Likely benign (Apr 10, 2014)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000312220	PreventionGenetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	11	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Free the data: one laboratory's approach to knowledge-based genomic variant classification and preparation for EMR integration of genomic data.

Bean LJ, Tinker SW, da Silva C, Hegde MR.

Hum Mutat. 2013 Sep;34(9):1183-8. doi: 10.1002/humu.22364. Epub 2013 Aug 5.

PubMed [citation]

PMID:: 23757202

ACMG recommendations for standards for interpretation and reporting of sequence variations: Revisions 2007.

Richards CS, Bale S, Bellissimo DB, Das S, Grody WW, Hegde MR, Lyon E, Ward BE; Molecular Subcommittee of the ACMG Laboratory Quality Assurance Committee..

Genet Med. 2008 Apr;10(4):294-300. doi: 10.1097/GIM.0b013e31816b5cae.

PubMed [citation]

PMID:: 18414213

See all PubMed Citations (3)

Details of each submission

From EGL Genetic Diagnostics,Eurofins Clinical Diagnostics, SCV000113602.6

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	11	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		11	not provided	not provided	not provided

From GeneDx, SCV000169860.10

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Genetic Services Laboratory, University of Chicago, SCV000195500.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From PreventionGenetics, SCV000312220.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Nov 4, 2017

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